Now I have to simulate it with LTspice, but it doesn't work. The output of the FFs is always 0. Can you help me?
I simulated the circuit with an other logic simulator and it works, i don't know if I set some wrong value.
Thank you.

Attached Files:

I remake the circuit using D FF (i change cause may the jkff downloaded from LTspice group don't works).

Equations:
D1=Q1 Q0' X' + Q1' Q0 X'
D0=X + Q1 Q0'
Z=Q1 Q0 X

I set the source V2 for the sequence 1001 (1st clock high value, 2nd and 3rd low value and 4th clock hight again). But when I start the simulation I have an error: "Analysis: Time step too small; time = 0.00012, timestep = 1.25e-019: trouble with dflop-instence a2"

Thank you

Attached Files:

I ran your first circuit by hand and I disagree with something:
You have the state 00 as the Reset state.
With a '1' you go to 01 and you start reading the '1001' sequence.
A '0' drives you to 10.
Another 0 gets you to 11.
And then with the final '1' you go to 01, which should be your final state but it has been used before.

I understand that you tried to build a Mealy machine, but to be honest I don't trust them much in actual fast circuits. I would use a fifth state even though that would add another Flip Flop.

That said, your JK circuit works in theory as you would like to, but I don't know what problems your software might cause. Maybe you could make the input last a bit longer, in order to avoid gate delays and propagation of them.

For example, make a clock tick every 1ms and synchronize your input in the same period and make your '1's last at about half a ms.